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Expressed sequence tag databases | Gene expression data analysis

Expressed sequence tags (ESTs) are short DNA sequences (200–500 nucleotides) generated by sequencing the 5′ and/or 3′ ends of cDNAs that are subsequently clustered and counted (Adams et al., 1991). Source text: Feichtinger et al.,…
CGD
Dataset

CGD Cucurbit Genomics Database

A database which offers gene annotation of cucurbit. This base offers the…

A database which offers gene annotation of cucurbit. This base offers the genome of Melon (Cucumis melo), Cucumber (Cucumis sativus), Watermelon (Citrullus lanatus), Pumpkin (Cucurbita maxima). The…

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NCBI dbEST
Dataset

NCBI dbEST

A division of GenBank that contains sequence data and other information on…

A division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.

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NCBI UniGene
Dataset

NCBI UniGene

Identifies transcripts from the same locus; analyzes expression by age, tissue…

Identifies transcripts from the same locus; analyzes expression by age, tissue and health status; and clone resources and reports related proteins (protEST).

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PEDE
Dataset

PEDE Pig EST Data Explorer

Provides information about cDNA sequences. PEDE contains more than 68 000…

Provides information about cDNA sequences. PEDE contains more than 68 000 high-quality expressed sequence tag (EST) collected from additional libraries. PEDE works with an Internet-based search…

TriTrypDB
Dataset

TriTrypDB

An integrated database providing access to genome-scale datasets for…

An integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs.

ToxoDB
Dataset

ToxoDB

A genome and functional genomic database for the protozoan parasite Toxoplasma…

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii.

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HGPD
Dataset

HGPD Human Gene and Protein Database

Compiles a set of protein expression and protein synthesis data added to human…

Compiles a set of protein expression and protein synthesis data added to human Gateway entry clones. HGPD compiles more than 40000 entry clones splitted in 10 protein function groups. The database…

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NEMBASE
Dataset

NEMBASE

A comprehensive Nematode Transcriptome Database including 63 nematode species,…

A comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins.

FLAGdb++
Dataset

FLAGdb++

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the…

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant…

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CR-EST
Dataset

CR-EST CRop EST database

Provides access to sequence, classification, clustering and annotation data of…

Provides access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200,000 sequences derived from 48 cDNA libraries of six species:…

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Pleurochrysome
Dataset

Pleurochrysome

Stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from…

Stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences…

PigGIS
Dataset

PigGIS Pig Genomic Informatics System

Furnishes pig gene annotations in all sequenced genomic regions. PigGIS gathers…

Furnishes pig gene annotations in all sequenced genomic regions. PigGIS gathers 3.84 million whole genome shotgun (WGS) records generated by the Sino–Danish Pig Genome Project, 870 084 expressed…

RiceGeneThreshe…
Dataset

RiceGeneThresher

A public online resource for mining genes underlying genome regions of interest…

A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome.

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Cassava Online…
Dataset

Cassava Online Archive

Provides expressed sequence tags (ESTs) currently available from NCBI…

Provides expressed sequence tags (ESTs) currently available from NCBI (Genbank/EMBL/DDBJ) and cassava mRNA sequences and their annotations. Cassava Online Archive simplifies the cassava genomics…

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ocsESTdb
Dataset

ocsESTdb

Collects oil crop seed ESTs and unigenes from B. napus, G. max, S. indicum and…

Collects oil crop seed ESTs and unigenes from B. napus, G. max, S. indicum and A. hypogaea and supplies a public resource for researchers to comparatively analyse and investigate oil accumulation…

PlantGDB
Dataset

PlantGDB

A genomics database encompassing sequence data for green plants (Viridiplantae).

A genomics database encompassing sequence data for green plants (Viridiplantae).

SGN
Dataset

SGN SOL Genomics Network

A Clade Oriented Database (COD) containing genomic, genetic, phenotypic and…

A Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for plant genomes.

Hevea…
Dataset

Hevea brasiliensis

A database which offers gene annotation of Hevea brasiliensis. The rubber tree…

A database which offers gene annotation of Hevea brasiliensis. The rubber tree is the major commercial source of natural rubber. The transcriptome was sequenced from vegetative shoot apex yielding…

OrchidBase
Dataset

OrchidBase

Hosts a comprehensive collection of Orchidaceae floral transcriptomes. The…

Hosts a comprehensive collection of Orchidaceae floral transcriptomes. The OrchidBase is a collection of 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among…

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SABRE2
Dataset

SABRE2 Systematic consolidation of Arabidopsis and other Botanical Resources

Cross-searches plant genetic resources through publicly available Arabidopsis…

Cross-searches plant genetic resources through publicly available Arabidopsis information. In SABRE, plant expressed sequence tag (EST)/cDNA clones are related to TAIR (The Arabidoposis Information…

RadishBase
Dataset

RadishBase

A genomics and genetics database of radish. RadishBase contains radish…

A genomics and genetics database of radish. RadishBase contains radish mitochondrial genome sequences, expressed sequence tag (EST) and unigene sequences and annotations, biochemical pathways,…

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XenDB
Dataset

XenDB

Allows individual and batch queries using Xenopus accession, GI, and XenDB,…

Allows individual and batch queries using Xenopus accession, GI, and XenDB, UniGene and TIGR cluster IDs. The XenDB database is designed to address a critical issue facing many researchers: the…

KONAGAbase
Dataset

KONAGAbase

Provides DBM comprehensive transcriptomic and draft genomic sequences with…

Provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target…

MorusDB
Dataset

MorusDB Morus genome database

Provides important genomic resources for scientists working with mulberry and…

Provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops.

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ClonorESTdb
Dataset

ClonorESTdb

Represents a collection of Clonorchis sinensis ESTs that is intended as a…

Represents a collection of Clonorchis sinensis ESTs that is intended as a resource for parasite functional genomics. ClonorESTdb enables the researcher to identify and compare expression signatures…

CancerEST
Dataset

CancerEST

A user-friendly and intuitive web-based tool for the automated identification…

A user-friendly and intuitive web-based tool for the automated identification of candidate cancer markers/targets, for examining tissue specificity as well as for integrated expression profiling.

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WikiCell
Dataset

WikiCell

Provides a unified view of the human transcriptome. WikiCell is an open and…

Provides a unified view of the human transcriptome. WikiCell is an open and public platform dedicated to the annotation of the human transcriptome. Researchers can contribute transcriptome data,…

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ANEXdb
Dataset

ANEXdb

Handles both microarray expression data and sequence assembly and annotation…

Handles both microarray expression data and sequence assembly and annotation data. ANEXdb is an open-source web application that supports integrated access of two databases that house microarray…

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PMPj-Blast
Dataset

PMPj-Blast

Offers data from were obtained from PMPj. PMPj-Blast is a database of…

Offers data from were obtained from PMPj. PMPj-Blast is a database of nucleotide sequences of Expressed Sequence tags (ESTs), cDNAs and oligo DNA microarray probes for Lotus japonicus and Arabidopsis…

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FLJ Human cDNA…
Dataset

FLJ Human cDNA Database

Provides a database based on "Sequence ID" and "Clone ID".…

Provides a database based on "Sequence ID" and "Clone ID". FLJ Human cDNA Database is a resource where user can search human full-length cDNAs in DB by sequence ID, Expressed…

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RefEx
Dataset

RefEx

Offers reference gene expression datasets of human, mouse, and rat. RefEx…

Offers reference gene expression datasets of human, mouse, and rat. RefEx focuses on tissues and cells of those species. It follows different measurement strategies: expressed sequence tag (EST),…

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bex-db
Dataset

bex-db Barley Gene Expression Database

A repository of transcriptome data including the sequences and the expression…

A repository of transcriptome data including the sequences and the expression profiles of barley genes resulting from microarray analysis. The bex-db should provide a useful resource for further…

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NRESTdb
Dataset

NRESTdb

Consists of EST sequences, BLASTX search results against the non-redundant…

Consists of EST sequences, BLASTX search results against the non-redundant protein database (NR), Pfam and InterPro, annotations based on KOG, Inparanoid and GO classifications, enhanced datasets…

PlasmoDB
Dataset

PlasmoDB

Provides a resource for data analysis and visualization in a gene-by-gene or…

Provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB is a functional genomic database for Plasmodium spp. It belongs to a family of genomic…

GiardiaDB
Dataset

GiardiaDB

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the…

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the WBC6 clinical isolate of G. lamblia. It is accessed via the standard EuPathDB web interface, providing a wide variety…

CryptoDB
Dataset

CryptoDB

A community bioinformatics resource for the AIDS-related apicomplexan-parasite,…

A community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium.

FungiDB
Dataset

FungiDB

A functional genomic resource for pan-fungal genomes that was developed in…

A functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center.

AmoebaDB
Dataset

AmoebaDB

Functional genomic databases serving the amoebozoa research communities.

Functional genomic databases serving the amoebozoa research communities.

MicrosporidiaDB
Dataset

MicrosporidiaDB

Functional genomic databases serving the microsporidia research communities.

Functional genomic databases serving the microsporidia research communities.

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BodyMap-Xs
Dataset

BodyMap-Xs

Allows cross-species gene expression comparison. BodyMap-Xs is a database that…

Allows cross-species gene expression comparison. BodyMap-Xs is a database that contains the anatomical breakdowns of about 17 million expressed sequence tags (ESTs) across animal species generated by…

SchistoDB
Dataset

SchistoDB

Provides a rich resource of genomic data for key blood flukes (genus…

Provides a rich resource of genomic data for key blood flukes (genus Schistosoma) which cause disease in hundreds of millions of people worldwide.

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CleanEST
Dataset

CleanEST

Stores raw and cleans expressed sequence tag (EST) classified in EST division…

Stores raw and cleans expressed sequence tag (EST) classified in EST division of GenBank (dbEST) libraries. CleanEST is a web-based database server that provides two different cleansed sequences for…

PiroplasmaDB
Dataset

PiroplasmaDB

A genome database for the genus Piroplasma. PiroplasmaDB is a member of…

A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

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CoffeebEST
Dataset

CoffeebEST Coffee Bean EST

A website and repository of EST comparisons focused on giving a user-friendly…

A website and repository of EST comparisons focused on giving a user-friendly analysis of bean EST data. CoffeebEST represents an additional resource for the coffee scientific community, offering a…

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CAGBASE
Dataset

CAGBASE Camel Genome Database

Contains annotated EST sequences and analysis tools with possibility to add…

Contains annotated EST sequences and analysis tools with possibility to add sequences from public domain. CAGBASE provides over 4,500 potentially novel or fast evolving camel gene sequences that do…

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ForestTreeDB
Dataset

ForestTreeDB

Provides a library of sequence annotation involved in tree research. and a…

Provides a library of sequence annotation involved in tree research. and a flexible interface for developing queries. ForestTreeDB contains more than 344 878 sequences from loblolly pine, white…

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STACKe
Dataset

STACKe Sequence Tag Alignment and Consensus Knowledgebase

A database for detection and visualisation of expressed transcript variation in…

A database for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. STACK organises and reconstructs human transcripts from available…

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